CT45A3

Summary

CT45A3 (cancer/testis antigen family 45 member A3, HGNC:33268) is a protein-coding gene on chromosome Xq26.3, encoding Cancer/testis antigen family 45 member A3 (Q8NHU0).

Located in nucleus.

Source: NCBI Gene 441519 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_001370148

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33268
Approved symbol	CT45A3
Name	cancer/testis antigen family 45 member A3
Location	Xq26.3
Locus type	gene with protein product
Status	Approved
Aliases	CT45-3, CT45.3, CT45-4, CT45.4
Ensembl gene	ENSG00000269096
Ensembl biotype	protein_coding
OMIM	300794
Entrez	441519

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000597510, ENST00000598716

RefSeq mRNA: 3 — MANE Select: NM_001370148 NM_001017435, NM_001370148, NM_001370149

CCDS: CCDS76030

Canonical transcript exons

ENST00000598716 — 5 exons

Exon	Start	End
ENSE00001830036	135768108	135768191
ENSE00003017646	135761634	135761727
ENSE00003038936	135762108	135762356
ENSE00003193431	135760044	135760409
ENSE00003718024	135764276	135764450

Expression profiles

Bgee: expression breadth broad, 41 present calls, max score 90.16.

Top tissues by expression

122 total, by Bgee expression score (0-100, higher = more expressed):

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	90.16	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	89.06	gold quality
right testis	UBERON:0004534	78.45	gold quality
testis	UBERON:0000473	75.34	gold quality
left testis	UBERON:0004533	73.87	gold quality
Ammon’s horn	UBERON:0001954	50.71	gold quality
prefrontal cortex	UBERON:0000451	48.91	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	48.11	gold quality
nucleus accumbens	UBERON:0001882	47.43	gold quality
hypothalamus	UBERON:0001898	47.17	gold quality
caudate nucleus	UBERON:0001873	46.23	gold quality
putamen	UBERON:0001874	43.51	gold quality
substantia nigra	UBERON:0002038	43.48	gold quality
amygdala	UBERON:0001876	43.40	gold quality
temporal lobe	UBERON:0001871	43.21	gold quality
sural nerve	UBERON:0015488	42.50	gold quality
frontal cortex	UBERON:0001870	42.09	gold quality
cerebral cortex	UBERON:0000956	40.82	gold quality
brain	UBERON:0000955	39.94	gold quality
anterior cingulate cortex	UBERON:0009835	38.17	gold quality
Brodmann (1909) area 9	UBERON:0013540	37.84	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
bone marrow cell	CL:0002092	36.16	gold quality
adenohypophysis	UBERON:0002196	35.81	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	35.69	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
superior frontal gyrus	UBERON:0002661	35.08	gold quality
primary visual cortex	UBERON:0002436	33.82	silver quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.48

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

14 targeting CT45A3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-6833-3P	100.00	70.63	3197
HSA-MIR-4768-5P	100.00	69.49	2861
HSA-MIR-4455	100.00	65.48	1587
HSA-MIR-6845-3P	99.94	66.88	1439
HSA-MIR-3133	99.81	70.92	3506
HSA-MIR-586	99.65	70.40	2051
HSA-MIR-5006-5P	98.79	66.92	1246
HSA-MIR-5572	98.55	65.84	970
HSA-MIR-6819-5P	97.96	66.59	1071
HSA-MIR-3151-3P	97.80	66.16	479
HSA-MIR-6737-5P	97.75	66.54	1044
HSA-MIR-6812-5P	97.56	65.39	1059
HSA-MIR-3674	97.01	68.86	1171
HSA-MIR-6747-5P	96.17	64.99	743

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
mus_musculus	Ct45a	ENSMUSG00000064016
rattus_norvegicus	Ct45a9	ENSRNOG00000048059
drosophila_melanogaster	IntS6	FBGN0261383
caenorhabditis_elegans		WBGENE00000994

Paralogs (11): INTS6 (ENSG00000102786), INTS6L (ENSG00000165359), SAGE1 (ENSG00000181433), CT45A5 (ENSG00000228836), CT45A1 (ENSG00000268940), CT45A10 (ENSG00000269586), CT45A9 (ENSG00000270946), CT45A2 (ENSG00000271449), CT45A7 (ENSG00000273696), CT45A8 (ENSG00000278085), CT45A6 (ENSG00000278289)

Protein

Protein identifiers

Cancer/testis antigen family 45 member A3 — Q8NHU0 (reviewed: Q8NHU0)

Alternative names: Cancer/testis antigen 45-3, Cancer/testis antigen 45-4, Cancer/testis antigen 45A3, Cancer/testis antigen 45A4, Cancer/testis antigen family 45 member A4

All UniProt accessions (1): Q8NHU0

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Nucleus.

Tissue specificity. Testis specific. Expressed in cancer cell lines.

Similarity. Belongs to the CT45 family.

RefSeq proteins (3): NP_001017435, NP_001357077, NP_001357078 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029307	INT_SG_DDX_CT_C	Domain
IPR051113	Integrator_subunit6	Family

Pfam: PF15300

UniProt features (4 total): chain 1, region of interest 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8NHU0-F1	69.86	0.21

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 5 (showing top): chrXq26, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, HE_LIM_SUN_FETAL_LUNG_C0_MYOFIBROBLAST_1_CELL, HE_LIM_SUN_FETAL_LUNG_C0_MYOFIBROBLAST_2_CELL, RICKMAN_HEAD_AND_NECK_CANCER_B

GO Biological Process (0):

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (1): nucleus (GO:0005634)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membrane-bounded organelle	1

Protein interactions and networks

STRING

0 interactions, top by confidence (×1000):

IntAct

29 interactions, top by confidence:

A	B	Type	Score
SDCBP2	CT45A3	psi-mi:“MI:0915”(physical association)	0.830
CT45A3	SDCBP2	psi-mi:“MI:0915”(physical association)	0.830
SDCBP	CT45A3	psi-mi:“MI:0915”(physical association)	0.720
CT45A3	SDCBP	psi-mi:“MI:0915”(physical association)	0.720
SF3B1	SAP18	psi-mi:“MI:0914”(association)	0.640
CT45A3	DVL3	psi-mi:“MI:0915”(physical association)	0.560
SUPT5H	POLR2D	psi-mi:“MI:0914”(association)	0.530
PPP4R2	TRAPPC13	psi-mi:“MI:0914”(association)	0.350
COPS7A	BTBD10	psi-mi:“MI:0914”(association)	0.350
PPP4C	ISG15	psi-mi:“MI:0914”(association)	0.350
PPP4R2	KRIT1	psi-mi:“MI:0914”(association)	0.350
TP53BP1	PSMD14	psi-mi:“MI:2364”(proximity)	0.270
BRCA1	SMCHD1	psi-mi:“MI:2364”(proximity)	0.270
CT45A3	DVL3	psi-mi:“MI:0915”(physical association)	0.000
CT45A3	SDCBP2	psi-mi:“MI:0915”(physical association)	0.000
CT45A3	SDCBP	psi-mi:“MI:0915”(physical association)	0.000
SDCBP	CT45A3	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (11): CT45A3 (Two-hybrid), CT45A3 (Two-hybrid), CT45A3 (Two-hybrid), CT45A3 (Affinity Capture-MS), CT45A3 (Two-hybrid), CT45A3 (Two-hybrid), CT45A3 (Two-hybrid), CT45A3 (Affinity Capture-MS), CT45A3 (Affinity Capture-MS), CT45A3 (Affinity Capture-MS), CT45A3 (Proximity Label-MS)

ESM2 similar proteins: A0FKI7, A2YX04, A5WUN7, A5WV69, A7J1T2, C5DZR8, E9Q555, F4J6F6, O43310, O48767, P0DMS1, P0DMU7, P0DMU8, P0DMU9, P0DMV0, P0DMV1, P0DMV2, Q0V9S3, Q12912, Q14693, Q1LXZ9, Q2NKQ1, Q2PFD7, Q3TEL6, Q502L1, Q5DJT8, Q5R7V3, Q5T8D3, Q5XG73, Q621Z7, Q640U0, Q641E3, Q6IRN6, Q6Z8M8, Q700C2, Q758T8, Q80Y56, Q811D2, Q8AV28, Q8BLN6

Diamond homologs: A6NJ88, P0DMU7, P0DMU8, P0DMU9, P0DMV0, P0DMV1, P0DMV2, Q2TAF4, Q5DJT8, Q5HYN5, Q5JSJ4, Q5U4W6, Q6PCM2, Q7SYD9, Q8BND4, Q8NHU0, Q9NXZ1, Q9UL03, Q54Z23, Q9W485

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

11 variants total. Per-class counts are floors (≥ shown; pagination cap):

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	9
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

374 predictions. Top by Δscore:

Variant	Effect	Δscore
X:135764275:GA:G	donor_gain	1.0000
X:135764269:G:GG	donor_gain	0.9900
X:135764272:T:G	donor_loss	0.9900
X:135764273:G:GG	donor_gain	0.9900
X:135764274:AGTA:A	donor_loss	0.9900
X:135764275:GAG:G	donor_gain	0.9900
X:135764276:AGA:A	donor_gain	0.9900
X:135764277:AAGA:A	donor_gain	0.9900
X:135764278:AAAGA:A	donor_gain	0.9900
X:135764449:G:GC	acceptor_loss	0.9900
X:135764449:G:GG	acceptor_gain	0.9900
X:135764449:GG:G	acceptor_gain	0.9900
X:135764449:GGAA:G	acceptor_gain	0.9900
X:135764449:GGAAA:G	acceptor_gain	0.9900
X:135764450:A:AG	acceptor_gain	0.9900
X:135764450:AG:A	acceptor_gain	0.9900
X:135764450:AGG:A	acceptor_loss	0.9900
X:135764451:CAG:C	acceptor_loss	0.9900
X:135764452:TCAGG:T	acceptor_loss	0.9900
X:135764453:TTCAG:T	acceptor_loss	0.9900
X:135764454:TTTCA:T	acceptor_loss	0.9900
X:135764271:A:AG	donor_loss	0.9800
X:135767890:A:T	donor_gain	0.9800
X:135764449:GGA:G	acceptor_gain	0.9700
X:135767937:GACTG:G	donor_gain	0.9600
X:135767938:GGACT:G	donor_gain	0.9600
X:135764270:A:AG	donor_gain	0.9400
X:135765848:A:T	donor_gain	0.9200
X:135764276:AGAGT:A	donor_gain	0.9000
X:135767933:G:GG	donor_gain	0.8900

AlphaMissense

1260 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
X:135761641:C:G	A169P	0.885
X:135761711:G:C	F145L	0.858
X:135761711:G:T	F145L	0.858
X:135761713:A:G	F145L	0.858
X:135764397:A:C	F16L	0.848
X:135764397:A:T	F16L	0.848
X:135764399:A:G	F16L	0.848
X:135762145:T:A	K127N	0.837
X:135762145:T:G	K127N	0.837
X:135761689:C:G	G153R	0.831
X:135761689:C:T	G153R	0.831
X:135761660:A:C	F162L	0.821
X:135761660:A:T	F162L	0.821
X:135761662:A:G	F162L	0.821
X:135761663:A:C	F161L	0.771
X:135761663:A:T	F161L	0.771
X:135761665:A:G	F161L	0.771
X:135761703:A:T	L148H	0.771
X:135762157:A:C	N123K	0.753
X:135762157:A:T	N123K	0.753
X:135761664:A:G	F161S	0.738
X:135762137:A:G	L130S	0.729
X:135760391:A:C	F177L	0.726
X:135760391:A:T	F177L	0.726
X:135760393:A:G	F177L	0.726
X:135764355:C:A	R30S	0.722
X:135764355:C:G	R30S	0.722
X:135760380:A:G	L181P	0.713
X:135761656:A:G	S164P	0.713
X:135764373:A:C	S24R	0.705

dbSNP variants (sampled 300 via entrez): RS1157444843 (X:135762865 C>A,T), RS1159567879 (X:135765963 AG>A), RS1159873872 (X:135760305 C>T), RS1161402331 (X:135763043 G>A), RS1162505828 (X:135762884 C>T), RS1164679150 (X:135760791 C>G,T), RS1166764359 (X:135763112 C>T), RS1166993855 (X:135759618 C>G,T), RS1167571698 (X:135765167 G>A), RS1168915208 (X:135760834 G>A), RS1171025699 (X:135759818 G>A), RS1171076552 (X:135759672 TTAATGTGTGTGTAAAA>T), RS1171900195 (X:135765498 A>C), RS1172105453 (X:135761991 T>A), RS1173763686 (X:135762779 A>C)

Disease associations

OMIM: gene MIM:300794 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

7 total (human), top 7 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	decreases expression	1
CGP 52608	affects binding, increases reaction	1
Cadmium	decreases expression	1
Copper	affects binding, decreases expression	1
Disulfiram	affects binding, decreases expression	1
Valproic Acid	increases methylation	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.